Commit 9d77e653 authored by Gerald Salin's avatar Gerald Salin
Browse files

Merge branch 'methylseq' into 'master'

Methylseq

See merge request !12
parents ff867bc4 b8ff28c8
......@@ -42,12 +42,12 @@ class RemoveDuplicate (Analysis):
if self.get_memory() != None :
self.mem=self.get_memory()
self.add_output_file_list("flagstat_init", "Flagstat initialy", pattern='{basename_woext}.init_flagstat', items=self.bam)
self.add_output_file_list("flagstat_rmdup", "Flagstat result after rmdup", pattern='{basename_woext}.rmdup_flagstat', items=self.bam)
self.add_output_file_list("flagstat_finally", "Flagstat result after removing singleton", pattern='{basename_woext}.finally_flagstat', items=self.bam)
if self.is_paired:
self.add_output_file_list("flagstat_rmdup", "Flagstat result after rmdup", pattern='{basename_woext}.rmdup_flagstat', items=self.bam)
self.add_output_file_list("rmdup_stderr", "The error trace file", pattern='{basename_woext}_rmdup.stderr', items=self.bam)
self.add_output_file_list("output", "The bam with removed duplicates (and singleton if paired)", pattern='{basename_woext}_clean.bam', items=self.bam)
self.add_output_file_list("rmdup_stderr", "The error trace file", pattern='{basename_woext}_rmdup.stderr', items=self.bam)
self.add_output_file_list("rmsinglet_stderr","The error trace file", pattern='{basename_woext}_rmsinglet.stderr', items=self.bam)
def define_analysis(self):
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment